Review
Cell Biology
Gustavo Satoru Kajitani, Livia Luz de Souza Nascimento, Maira Rodrigues de Camargo Neves, Giovana da Silva Leandro, Camila Carriao Machado Garcia, Carlos Frederico Martins Menck
Summary: This article reviews the evidence on mechanisms related to neurodegenerative processes associated with DNA damage responses. The focus is on the effects of the transcription machinery, including the accumulation of DNA·RNA hybrids (R-loops) that influence DNA damage and repair metabolism. Neuronal tissues with higher expression of long genes may be more affected by DNA lesions, potentially explaining part of the neurological abnormalities observed in patients.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Yuliya Krasikova, Nadejda Rechkunova, Olga Lavrik
Summary: Nucleotide excision repair (NER) is a versatile DNA repair pathway that is linked to neurological degeneration in patients with Xeroderma pigmentosum. Xeroderma pigmentosum patients typically have a high sensitivity to ultraviolet light due to DNA repair defects, leading to multiple skin and eye cancers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Juan Antonio Garcia-Carmona, Matthew J. Yousefzadeh, Fernando Alarcon-Soldevilla, Eva Fages-Caravaca, Tra L. Kieu, Mariah A. Witt, Angel Lopez-Avila, Laura J. Niedernhofer, Jose Antonio Perez-Vicente
Summary: The study aimed to diagnose neurological impairment in adolescent patients, identifying xeroderma pigmentosum (XP) through whole-exome sequencing. Genetic analysis revealed recessive mutations in XPA affecting nucleotide excision repair (NER) capacity. The significantly impaired NER in the patient underscores the importance of considering XP in differential diagnosis for atypical neurodegeneration.
FRONTIERS IN GENETICS
(2021)
Review
Biochemistry & Molecular Biology
Jiahui Zhu, Lexin Liu, Xiaodi Ma, Xinyu Cao, Yu Chen, Xiangping Qu, Ming Ji, Huijun Liu, Chi Liu, Xiaoqun Qin, Yang Xiang
Summary: The mortality rate of idiopathic pulmonary fibrosis (IPF) increases yearly due to ineffective treatment. Oxidative stress, especially DNA stimulation, plays a crucial role in pulmonary fibrosis. DNA damage is important in the initiation of IPF and DNA repair systems targeting damage are crucial for lung cell survival. However, existing research has not focused on the role of DNA damage and repair pathways in IPF.
Article
Biochemistry & Molecular Biology
Ashan P. Wettasinghe, Melodee O. Seifi, Marco Bravo, Austen C. Adams, Aman Patel, Monica Lou, Dimithree Kahanda, Hao-Che Peng, Allison L. Stelling, Li Fan, Jason D. Slinker
Summary: DNA helicase activity is crucial for various DNA metabolic processes. This study investigates the binding and activity of helicases StXPB2 and AfXPB, revealing a concentration-dependent activity for AfXPB and a crossover between fast molecular wrench and slower conventional helicase modes. The AfXPB-Bax1 complex inhibits rapid activity, while the StXPB2-Bax1 complex induces rapid kinetics at higher concentrations.
Review
Biochemistry & Molecular Biology
Nicolas Nieto Moreno, Anouk M. Olthof, Jesper Q. Svejstrup
Summary: UV irradiation and other genotoxic stresses can cause bulky DNA lesions, posing a threat to genome stability and cell viability. Two main repair pathways, GG-NER and TC-NER, have evolved in cells to remove such lesions. This study summarizes the current understanding of these repair mechanisms, focusing on the roles of stalled RNA polymerase II, CSB, CSA, and UVSSA in TC-NER. It also discusses the involvement of protein ubiquitylation and the impact of UV irradiation on transcription, as well as the pathogenic mechanisms of xeroderma pigmentosum and Cockayne syndrome.
ANNUAL REVIEW OF BIOCHEMISTRY
(2023)
Article
Oncology
Carmen Ortiz-Sanchez, Jarline Encarnacion-Medina, Jong Y. Park, Natasha Moreno, Gilberto Ruiz-Deya, Jaime Matta
Summary: This study evaluated variations in DNA repair capacity (DRC) in Puerto Rican men with prostate cancer (PCa). The results showed that PCa cases had lower DRC levels compared to controls. Additionally, DRC levels may have the potential to discriminate between aggressive and indolent PCa cases.
Article
Multidisciplinary Sciences
Chao Chen, Haozhen Liu, Yanlin Li, Jixian Liu
Summary: This study found that ERCC mutations are associated with tumor prognosis and the response to immune checkpoint inhibitors (ICI). Patients with ERCC mutations showed improved survival and higher tumor mutation burden. These patients also had better clinical outcomes and higher response rates when undergoing ICI therapy. Further analysis revealed increased tumor neoantigen burden and immune-response cell infiltration in patients with ERCC mutations.
SCIENTIFIC REPORTS
(2023)
Review
Genetics & Heredity
Apurva Barve, Alisha A. Galande, Saroj S. Ghaskadbi, Surendra Ghaskadbi
Summary: Hydra, discovered in 1744, has become a popular research organism due to its remarkable regeneration capacity, unique tissue dynamics, continuous pattern formation, evolutionary position, and apparent lack of senescence. While there has been extensive research in the field of evolutionary developmental biology of hydra, recent focus has shifted to molecular mechanisms underlying various phenomena. Analysis of DNA repair mechanisms in hydra has revealed high similarity with vertebrate orthologues, hinting at ancient evolutionary origins and highlighting the importance of studying repair components and functions in this early metazoan.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Mihyun Kim, Hyun-Suk Kim, Areetha D'Souza, Kaitlyn Gallagher, Eunwoo Jeong, Kateryna Ogorodnik Le Meur, Chi-Lin Tsai, Miaw-Sheue Tsai, Minyong Kee, John A. Tainer, Jung-Eun Yeo, Walter J. Chazin, Orlando D. Scharer
Summary: The XPA and RPA proteins play essential roles in the assembly of the preincision complex in the nucleotide excision repair pathway. Mutations in the interaction sites of XPA and RPA inhibit the physical interaction and reduce the NER activity. The interaction between XPA-N and RPA32C is important for the initial association of XPA with NER complexes, while the interaction between XPA DBD and RPA70AB is needed for structural organization of the complex to license the dual incision reaction. The shape of the NER bubble is not colinear as previously thought, but rather the unwound DNA assumes a U-shape with the junctions localized in close proximity. The interaction between XPA and RPA70 is key for the organization of the NER preincision complex.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Magdalena P. Crossley, Chenlin Song, Michael J. Bocek, Jun-Hyuk Choi, Joseph Kousorous, Ataya Sathirachinda, Cindy Lin, Joshua R. Brickner, Gongshi Bai, Hannes Lans, Wim Vermeulen, Monther Abu-Remaileh, Karlene A. Cimprich
Summary: R-loops are RNA-DNA hybrids with important cellular roles, but their deregulation can lead to DNA damage. This study identifies a new population of cytoplasmic RNA-DNA hybrids that are processed from nuclear R-loops. These cytoplasmic hybrids activate innate immune response and induce cell death. Aberrant R-loop processing and innate immune activation may contribute to various diseases.
Article
Microbiology
Florent Ailloud, Iratxe Estibariz, Gudrun Pfaffinger, Sebastian Suerbaum
Summary: Helicobacter pylori is a common and genetically diverse human bacterial pathogen responsible for chronic gastritis and gastric cancer. The integration of short DNA fragments in H. pylori during natural transformation is determined by the UvrC endonuclease, suggesting distinct pathways for importing short and long fragments.
Review
Biochemistry & Molecular Biology
Vladimir Shafirovich, Nicholas E. Geacintov
Summary: Base excision repair (BER) and nucleotide excision repair (NER) are two major mechanisms that remove DNA lesions. Experimental evidence shows that oxidatively generated DNA lesions can be repaired by both competitive BER and NER pathways. The interaction between BER and NER pathways in repairing oxidatively generated DNA lesions is crucial for understanding DNA repair mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Anatoly A. Bulygin, Victoria N. Syryamina, Aleksandra A. Kuznetsova, Darya S. Novopashina, Sergei A. Dzuba, Nikita A. Kuznetsov
Summary: This study investigated the molecular events in the process of damage recognition by Apurinic/apyrimidinic endonuclease 1 (APE1) through DEER spectroscopy and kinetic analysis. The results showed that specific mutants of APE1 had higher activity in recognizing and repairing damaged DNA, revealing the factors that affect its substrate specificity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Pharmacology & Pharmacy
Geng Wang, Hongmin Guo, Yan Ren, Weiyi Chen, Yixuan Wang, Jianing Li, Hua Liu, Jingjun Xing, Yanru Zhang, Na Li
Summary: This study investigates the effects and mechanisms of triptolide (TPL) and carboplatin (CBP) in treating melanoma. The results demonstrate that the combination of TPL and CBP can selectively inhibit NER pathway activity and synergistically inhibit the viability, migration, invasion, and induce apoptosis of melanoma cells. Additionally, combined treatment with TPL and CBP can significantly suppress tumor progression in nude mice by inhibiting cell proliferation and inducing apoptosis.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Genetics & Heredity
Marit A. E. van Bueren, Aniek Janssen
Summary: Eukaryotic nuclei rely on multiple repair pathways to accurately repair DNA damage, particularly in chromatin domains enriched for repetitive DNA sequences. Tailored repair mechanisms are necessary to maintain genome stability in these domains.
